Support amplicon schemes in artic bed format #113
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Thanks for this! Working for me on master with the ARTIC v3 primer bed |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
If an amplicon scheme filename ends with ".bed" then it assumes it's in "artic bed" format, instead of viridian's usual tsv format.
For example: https://github.com/quick-lab/primerschemes/blob/main/primerschemes/artic-sars-cov-2/400/v5.3.2/primer.bed
Not really advertising this feature for now because there's no proper spec for that bed format (in particular, the naming convention used in column 4), but is requested by @bede.